chr13-103040879-T-C

Variant names:

• chr13-103040879-T-C
• rs1549836

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.882 in 152,204 control chromosomes in the GnomAD database, including 59,392 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (59392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134168 AN: 152086 Hom.: 59339 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.873

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.882 AC: 134274 AN: 152204 Hom.: 59392 Cov.: 32 AF XY: 0.879 AC XY: 65437 AN XY: 74434

African (AFR) AF: 0.927 AC: 38521 AN: 41550

American (AMR) AF: 0.812 AC: 12394 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3468

East Asian (EAS) AF: 0.740 AC: 3836 AN: 5186

South Asian (SAS) AF: 0.850 AC: 4098 AN: 4822

European-Finnish (FIN) AF: 0.882 AC: 9358 AN: 10612

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60079 AN: 67984

Other (OTH) AF: 0.875 AC: 1845 AN: 2108

Alfa AF: 0.898 Hom.: 9489

Bravo AF: 0.879

Asia WGS AF: 0.818 AC: 2839 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		-0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1549836; hg19: chr13-103693229;